diff options
| -rw-r--r-- | wqflask/wqflask/marker_regression/marker_regression.py | 5 | ||||
| -rw-r--r-- | wqflask/wqflask/marker_regression/rqtl_mapping.py | 35 |
2 files changed, 23 insertions, 17 deletions
diff --git a/wqflask/wqflask/marker_regression/marker_regression.py b/wqflask/wqflask/marker_regression/marker_regression.py index bb964961..f2a2eb8c 100644 --- a/wqflask/wqflask/marker_regression/marker_regression.py +++ b/wqflask/wqflask/marker_regression/marker_regression.py @@ -166,7 +166,10 @@ class MarkerRegression(object): self.model = start_vars['mapmodel_rqtl_geno'] if start_vars['pair_scan'] == "true": self.pair_scan = True - results = rqtl_mapping.run_rqtl_geno(self.vals, self.dataset, self.method, self.model, self.permCheck, self.num_perm, self.do_control, self.control_marker, self.manhattan_plot, self.pair_scan) + if self.permCheck and self.num_perm > 0: + perm_output, self.suggestive, self.significant, results = rqtl_mapping.run_rqtl_geno(self.vals, self.dataset, self.method, self.model, self.permCheck, self.num_perm, self.do_control, self.control_marker, self.manhattan_plot, self.pair_scan) + else: + results = rqtl_mapping.run_rqtl_geno(self.vals, self.dataset, self.method, self.model, self.permCheck, self.num_perm, self.do_control, self.control_marker, self.manhattan_plot, self.pair_scan) elif self.mapping_method == "reaper": if "startMb" in start_vars: #ZS: Check if first time page loaded, so it can default to ON if "additiveCheck" in start_vars: diff --git a/wqflask/wqflask/marker_regression/rqtl_mapping.py b/wqflask/wqflask/marker_regression/rqtl_mapping.py index 53ea6053..93bf717c 100644 --- a/wqflask/wqflask/marker_regression/rqtl_mapping.py +++ b/wqflask/wqflask/marker_regression/rqtl_mapping.py @@ -1,4 +1,5 @@ import rpy2.robjects as ro
+import numpy as np
from base.webqtlConfig import TMPDIR
from utility import webqtlUtil
@@ -72,9 +73,10 @@ def run_rqtl_geno(vals, dataset, method, model, permCheck, num_perm, do_control, else:
perm_data_frame = scanone(cross_object, pheno_col = "the_pheno", n_perm = num_perm, model=model, method=method)
- process_rqtl_perm_results(num_perm, perm_data_frame) # Functions that sets the thresholds for the webinterface
-
- return process_rqtl_results(result_data_frame)
+ perm_output, suggestive, significant = process_rqtl_perm_results(num_perm, perm_data_frame) # Functions that sets the thresholds for the webinterface
+ return perm_output, suggestive, significant, process_rqtl_results(result_data_frame)
+ else:
+ return process_rqtl_results(result_data_frame)
def geno_to_rqtl_function(dataset): # TODO: Need to figure out why some genofiles have the wrong format and don't convert properly
@@ -161,6 +163,19 @@ def process_pair_scan_results(result): return pair_scan_results
+def process_rqtl_perm_results(num_perm, results):
+ perm_vals = []
+ for line in str(results).split("\n")[1:(num_perm+1)]:
+ #print("R/qtl permutation line:", line.split())
+ perm_vals.append(float(line.split()[1]))
+
+ perm_output = perm_vals
+ suggestive = np.percentile(np.array(perm_vals), 67)
+ significant = np.percentile(np.array(perm_vals), 95)
+ print("SIGNIFICANT:", significant)
+
+ return perm_output, suggestive, significant
+
def process_rqtl_results(result): # TODO: how to make this a one liner and not copy the stuff in a loop
qtl_results = []
@@ -175,16 +190,4 @@ def process_rqtl_results(result): # TODO: how to make this a one liner an marker['lod_score'] = output[i][2]
qtl_results.append(marker)
- return qtl_results
-
-def process_rqtl_perm_results(num_perm, results):
- perm_vals = []
- for line in str(results).split("\n")[1:(num_perm+1)]:
- #print("R/qtl permutation line:", line.split())
- perm_vals.append(float(line.split()[1]))
-
- perm_output = perm_vals
- suggestive = np.percentile(np.array(perm_vals), 67)
- significant = np.percentile(np.array(perm_vals), 95)
-
- return perm_output, suggestive, significant
\ No newline at end of file + return qtl_results
\ No newline at end of file |